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Unmasking Novel Loci for Internal Phosphorus Utilization Efficiency in Rice Germplasm through Genome-Wide Association Analysis.

Wissuwa M, Kondo K, Fukuda T, Mori A, Rose MT, Pariasca-Tanaka J, Kretzschmar T, Haefele SM, Rose TJ - PLoS ONE (2015)

Bottom Line: Loci associated with PUE were mapped on chromosomes 1, 4, 11 and 12.The loci reported here are the first identified for PUE in any crop that is not confounded by differential P uptake among genotypes.Importantly, modern rice varieties lacked haplotypes associated with superior PUE, and would thus benefit from targeted introgressions of these loci from traditional donors to improve plant growth in phosphorus-limited cropping systems.

View Article: PubMed Central - PubMed

Affiliation: Crop, Livestock and Environment Division, Japan International Research Centre for Agricultural Science, Tsukuba, Ibaraki, Japan.

ABSTRACT
Depletion of non-renewable rock phosphate reserves and phosphorus (P) fertilizer price increases has renewed interest in breeding P-efficient varieties. Internal P utilization efficiency (PUE) is of prime interest because there has been no progress to date in breeding for high PUE. We characterized the genotypic variation for PUE present within the rice gene pool by using a hydroponic system that assured equal plant P uptake, followed by mapping of loci controlling PUE via Genome-Wide Association Studies (GWAS). Loci associated with PUE were mapped on chromosomes 1, 4, 11 and 12. The highest PUE was associated with a minor indica-specific haplotype on chromosome 1 and a rare aus-specific haplotype on chromosome 11. Comparative variant and expression analysis for genes contained within the chromosome 1 haplotype identified high priority candidate genes. Differences in coding regions and expression patterns between genotypes of contrasting haplotypes, suggested functional alterations for two predicted nucleic acid-interacting proteins that are likely causative for the observed differences in PUE. The loci reported here are the first identified for PUE in any crop that is not confounded by differential P uptake among genotypes. Importantly, modern rice varieties lacked haplotypes associated with superior PUE, and would thus benefit from targeted introgressions of these loci from traditional donors to improve plant growth in phosphorus-limited cropping systems.

No MeSH data available.


Related in: MedlinePlus

Deviation from the mean PUE for haplotype groups within the indica subpopulation.Labels on the x-axis (---,-+-, etc.) refer to having the negative or positive haplotype at each of the QTLs on chromosomes 1 (7.2Mb), 4 (17.8Mb) and 12 (26.6Mb), in that order (see Fig 3). Accessions in the ‘+++’ group include ‘Mudgo’, ‘Short Grain’ and ‘Yodanya’ while the ‘---‘ group are mostly older ‘modern’ varieties (IR8, Taichung Native, Teqing, Zhenshan2). The successful second generation green revolution varieties ‘IR36’ and ‘IR64’ belong to the ‘-+-’ group.
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pone.0124215.g004: Deviation from the mean PUE for haplotype groups within the indica subpopulation.Labels on the x-axis (---,-+-, etc.) refer to having the negative or positive haplotype at each of the QTLs on chromosomes 1 (7.2Mb), 4 (17.8Mb) and 12 (26.6Mb), in that order (see Fig 3). Accessions in the ‘+++’ group include ‘Mudgo’, ‘Short Grain’ and ‘Yodanya’ while the ‘---‘ group are mostly older ‘modern’ varieties (IR8, Taichung Native, Teqing, Zhenshan2). The successful second generation green revolution varieties ‘IR36’ and ‘IR64’ belong to the ‘-+-’ group.

Mentions: Three significant PUE loci were identified in the indica subpopulation (Fig 3), allowing for combined haplotype analysis (Fig 4): Having the unfavorable haplotype at three loci (---) for chromosomes 1 (7.2 Mb), 4 (17.8 Mb) and 12 (26.6 Mb) resulted in below-average PUE. Having at least one favorable haplotype (-+-) improved PUE to the overall average level while possessing three favorable haplotypes (+++) resulted in the best performance. The locus on chromosome 12 was only detected in Exp2 (Table 3) and hence, having a second positive haplotype on chromosome 12 (-++) improved performance in Exp2 but not in Exp1. Overall data suggest these three loci act at least partly in an additive manner.


Unmasking Novel Loci for Internal Phosphorus Utilization Efficiency in Rice Germplasm through Genome-Wide Association Analysis.

Wissuwa M, Kondo K, Fukuda T, Mori A, Rose MT, Pariasca-Tanaka J, Kretzschmar T, Haefele SM, Rose TJ - PLoS ONE (2015)

Deviation from the mean PUE for haplotype groups within the indica subpopulation.Labels on the x-axis (---,-+-, etc.) refer to having the negative or positive haplotype at each of the QTLs on chromosomes 1 (7.2Mb), 4 (17.8Mb) and 12 (26.6Mb), in that order (see Fig 3). Accessions in the ‘+++’ group include ‘Mudgo’, ‘Short Grain’ and ‘Yodanya’ while the ‘---‘ group are mostly older ‘modern’ varieties (IR8, Taichung Native, Teqing, Zhenshan2). The successful second generation green revolution varieties ‘IR36’ and ‘IR64’ belong to the ‘-+-’ group.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4414551&req=5

pone.0124215.g004: Deviation from the mean PUE for haplotype groups within the indica subpopulation.Labels on the x-axis (---,-+-, etc.) refer to having the negative or positive haplotype at each of the QTLs on chromosomes 1 (7.2Mb), 4 (17.8Mb) and 12 (26.6Mb), in that order (see Fig 3). Accessions in the ‘+++’ group include ‘Mudgo’, ‘Short Grain’ and ‘Yodanya’ while the ‘---‘ group are mostly older ‘modern’ varieties (IR8, Taichung Native, Teqing, Zhenshan2). The successful second generation green revolution varieties ‘IR36’ and ‘IR64’ belong to the ‘-+-’ group.
Mentions: Three significant PUE loci were identified in the indica subpopulation (Fig 3), allowing for combined haplotype analysis (Fig 4): Having the unfavorable haplotype at three loci (---) for chromosomes 1 (7.2 Mb), 4 (17.8 Mb) and 12 (26.6 Mb) resulted in below-average PUE. Having at least one favorable haplotype (-+-) improved PUE to the overall average level while possessing three favorable haplotypes (+++) resulted in the best performance. The locus on chromosome 12 was only detected in Exp2 (Table 3) and hence, having a second positive haplotype on chromosome 12 (-++) improved performance in Exp2 but not in Exp1. Overall data suggest these three loci act at least partly in an additive manner.

Bottom Line: Loci associated with PUE were mapped on chromosomes 1, 4, 11 and 12.The loci reported here are the first identified for PUE in any crop that is not confounded by differential P uptake among genotypes.Importantly, modern rice varieties lacked haplotypes associated with superior PUE, and would thus benefit from targeted introgressions of these loci from traditional donors to improve plant growth in phosphorus-limited cropping systems.

View Article: PubMed Central - PubMed

Affiliation: Crop, Livestock and Environment Division, Japan International Research Centre for Agricultural Science, Tsukuba, Ibaraki, Japan.

ABSTRACT
Depletion of non-renewable rock phosphate reserves and phosphorus (P) fertilizer price increases has renewed interest in breeding P-efficient varieties. Internal P utilization efficiency (PUE) is of prime interest because there has been no progress to date in breeding for high PUE. We characterized the genotypic variation for PUE present within the rice gene pool by using a hydroponic system that assured equal plant P uptake, followed by mapping of loci controlling PUE via Genome-Wide Association Studies (GWAS). Loci associated with PUE were mapped on chromosomes 1, 4, 11 and 12. The highest PUE was associated with a minor indica-specific haplotype on chromosome 1 and a rare aus-specific haplotype on chromosome 11. Comparative variant and expression analysis for genes contained within the chromosome 1 haplotype identified high priority candidate genes. Differences in coding regions and expression patterns between genotypes of contrasting haplotypes, suggested functional alterations for two predicted nucleic acid-interacting proteins that are likely causative for the observed differences in PUE. The loci reported here are the first identified for PUE in any crop that is not confounded by differential P uptake among genotypes. Importantly, modern rice varieties lacked haplotypes associated with superior PUE, and would thus benefit from targeted introgressions of these loci from traditional donors to improve plant growth in phosphorus-limited cropping systems.

No MeSH data available.


Related in: MedlinePlus